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I am processing my Single Cell RNA seq data and I am at Cluster Analysis:
FindConservedMarkers(seurat_integrated,
ident.1 = cluster,
grouping.var = "sample…
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Please see my code.
I can't help running my data with clustree
Even just
clustree (analysis)
analysis
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Hello, thanks for muon!
I was trying to reproduce the steps described in the ATAC tutorial (https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/2-Chromatin-Accessibility-Pr…
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https://mp.weixin.qq.com/s/3dZQxDdY6M1WwMMcus5Gkg
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Hi,
Thanks for the valuable tool.
I have a single cell RNA-seq dataset that includes:
3 samples healthy == 3 batches
3 samples patients == 3 batches
Can I build up a signature matrix by c…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/zhengxwen/SCArray.sat
Confirm the following by ed…
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Hi
Likely I have a lot of NAs in my TCR
`quantContig(combined, cloneCall="gene+nt", scale = T)`
![Rplot](https://user-images.githubusercontent.com/43682980/167117304-9496604e-b555-4bcd-98a2-87…
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Hello Scissor,
My scRNA-seq workflow is based on Scanpy. After Scanpy proceeded with my data, I saved it into h5ad file. Then, I use R Markdown to convert my hd5ad file into a Seurat object. Then run…
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I allowed myself to create a new issue since mine and Yulong don't seem to have the same answers after all. So, the two lines I respectively used to run braker1 and braker2 are :
braker.pl --genome=…
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Followed by a discussion with @franasa , @bussec; we have come up with the below schema for cell object.
```
Cell:
discriminator: AIRR
type: object
required:
- cell_id
…